Alignments for a candidate for leuA in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Escherichia coli BW25113

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate 14220 b0074 2-isopropylmalate synthase (NCBI)

Query= ecocyc::2-ISOPROPYLMALATESYN-MONOMER
         (523 letters)



>FitnessBrowser__Keio:14220
          Length = 523

 Score = 1023 bits (2645), Expect = 0.0
 Identities = 523/523 (100%), Positives = 523/523 (100%)

Query: 1   MSQQVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQT 60
           MSQQVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQT
Sbjct: 1   MSQQVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQT 60

Query: 61  IARQVKNSRVCALARCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSTLDEVIE 120
           IARQVKNSRVCALARCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSTLDEVIE
Sbjct: 61  IARQVKNSRVCALARCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSTLDEVIE 120

Query: 121 RAIYMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINAGATTINIPDTVGYTMPFEF 180
           RAIYMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINAGATTINIPDTVGYTMPFEF
Sbjct: 121 RAIYMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINAGATTINIPDTVGYTMPFEF 180

Query: 181 AGIISGLYERVPNIDKAIISVHTHDDLGLAVGNSLAAVHAGARQVEGAMNGIGERAGNCS 240
           AGIISGLYERVPNIDKAIISVHTHDDLGLAVGNSLAAVHAGARQVEGAMNGIGERAGNCS
Sbjct: 181 AGIISGLYERVPNIDKAIISVHTHDDLGLAVGNSLAAVHAGARQVEGAMNGIGERAGNCS 240

Query: 241 LEEVIMAIKVRKDILNVHTAINHQEIWRTSQLVSQICNMPIPANKAIVGSGAFAHSSGIH 300
           LEEVIMAIKVRKDILNVHTAINHQEIWRTSQLVSQICNMPIPANKAIVGSGAFAHSSGIH
Sbjct: 241 LEEVIMAIKVRKDILNVHTAINHQEIWRTSQLVSQICNMPIPANKAIVGSGAFAHSSGIH 300

Query: 301 QDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMDEMGYKESEYNLDNLYDAF 360
           QDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMDEMGYKESEYNLDNLYDAF
Sbjct: 301 QDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMDEMGYKESEYNLDNLYDAF 360

Query: 361 LKLADKKGQVFDYDLEALAFIGKQQEEPEHFRLDYFSVQSGSNDIATAAVKLACGEEVKA 420
           LKLADKKGQVFDYDLEALAFIGKQQEEPEHFRLDYFSVQSGSNDIATAAVKLACGEEVKA
Sbjct: 361 LKLADKKGQVFDYDLEALAFIGKQQEEPEHFRLDYFSVQSGSNDIATAAVKLACGEEVKA 420

Query: 421 EAANGNGPVDAVYQAINRITEYNVELVKYSLTAKGHGKDALGQVDIVANYNGRRFHGVGL 480
           EAANGNGPVDAVYQAINRITEYNVELVKYSLTAKGHGKDALGQVDIVANYNGRRFHGVGL
Sbjct: 421 EAANGNGPVDAVYQAINRITEYNVELVKYSLTAKGHGKDALGQVDIVANYNGRRFHGVGL 480

Query: 481 ATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQHNENNKETV 523
           ATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQHNENNKETV
Sbjct: 481 ATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQHNENNKETV 523


Lambda     K      H
   0.317    0.132    0.368 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 976
Number of extensions: 32
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 523
Length of database: 523
Length adjustment: 35
Effective length of query: 488
Effective length of database: 488
Effective search space:   238144
Effective search space used:   238144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate 14220 b0074 (2-isopropylmalate synthase (NCBI))
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00973.hmm
# target sequence database:        /tmp/gapView.14717.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 2-isopropylmalate synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.1e-264  861.9   8.5     7e-264  861.7   8.5    1.0  1  lcl|FitnessBrowser__Keio:14220  b0074 2-isopropylmalate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14220  b0074 2-isopropylmalate synthase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  861.7   8.5    7e-264    7e-264       1     494 []       4     497 ..       4     497 .. 1.00

  Alignments for each domain:
  == domain 1  score: 861.7 bits;  conditional E-value: 7e-264
                       TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekdid 79 
                                     +v+ifdttlrdGeqa++asl+v+eklqia+aler+gvd++e+Gfpvss+gdfe+vq+iar+vkn+rv++lar+vekdid
  lcl|FitnessBrowser__Keio:14220   4 QVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQTIARQVKNSRVCALARCVEKDID 82 
                                     699**************************************************************************** PP

                       TIGR00973  80 aaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvveaaiea 158
                                     +aae+lk+ae++rihtfiats++h+++kl++t dev+er++++vk+a+n++ddvefs+edagrt++++larvveaai+a
  lcl|FitnessBrowser__Keio:14220  83 VAAESLKVAEAFRIHTFIATSPMHIATKLRSTLDEVIERAIYMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINA 161
                                     ******************************************************************************* PP

                       TIGR00973 159 GattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGeraGnaa 237
                                     GattiniPdtvGy++P e++ +i++l+e+vPnidkai+svh+hddlGlav+nslaav++Garqve+++nGiGeraGn++
  lcl|FitnessBrowser__Keio:14220 162 GATTINIPDTVGYTMPFEFAGIISGLYERVPNIDKAIISVHTHDDLGLAVGNSLAAVHAGARQVEGAMNGIGERAGNCS 240
                                     ******************************************************************************* PP

                       TIGR00973 238 leevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesi 316
                                     leev+ma+kvrkd+lnv+t+in++ei+rts+lvs++++m++++nkaivG++afah+sGihqdGvlkn+e+yei++pesi
  lcl|FitnessBrowser__Keio:14220 241 LEEVIMAIKVRKDILNVHTAINHQEIWRTSQLVSQICNMPIPANKAIVGSGAFAHSSGIHQDGVLKNRENYEIMTPESI 319
                                     ******************************************************************************* PP

                       TIGR00973 317 GlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqv 395
                                     Gl++ +l+l++rsGraa+k+r++e+G+k++e++ld+l+++f++ladkk++vfd+dleal+++ ++qee e+++l++++v
  lcl|FitnessBrowser__Keio:14220 320 GLNQIQLNLTSRSGRAAVKHRMDEMGYKESEYNLDNLYDAFLKLADKKGQVFDYDLEALAFIGKQQEEPEHFRLDYFSV 398
                                     ******************************************************************************* PP

                       TIGR00973 396 qsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysG 474
                                     qsg+++++ta+vkl++ +e k++aa+GnGpvdavy+ai++i+e++v+l++ys+takg+gkdalg+v++v+++ng++++G
  lcl|FitnessBrowser__Keio:14220 399 QSGSNDIATAAVKLACGEEVKAEAANGNGPVDAVYQAINRITEYNVELVKYSLTAKGHGKDALGQVDIVANYNGRRFHG 477
                                     ****************7777*********************************************************** PP

                       TIGR00973 475 rgvatdiveasakayvnaln 494
                                     +g+atdive+saka+v++ln
  lcl|FitnessBrowser__Keio:14220 478 VGLATDIVESSAKAMVHVLN 497
                                     ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (523 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.26
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis